Gene Page:HOXD11

Summary?
GeneID 3237
Symbol HOXD11
Synonyms HOX4|HOX4F
Description homeobox D11
Reference MIM:142986|HGNC:HGNC:5134|Ensembl:ENSG00000128713|HPRD:00869|Vega:OTTHUMG00000132510
Gene type protein-coding
Map location 2 q31.1
Pascal p-value 0.033
Fetal beta -0.03
DMG 2 (# studies)
eGene Myers' cis & trans

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:PGCnp Genome-wide Association Study GWAS
DMG:Jaffe_2016 Genome-wide DNA methylation analysis This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 2
DMG:Wockner_2014 Genome-wide DNA methylation analysis This dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). 2

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg03782202 2 176971820 HOXD11 5.39E-5 -0.4 0.022 DMG:Wockner_2014
cg23895340 2 176973275 HOXD11 2.41E-8 -0.015 7.86E-6 DMG:Jaffe_2016

@eQTL annotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTL type
rs7972594 chr12 11724913 HOXD11 3237 0.09 trans
rs10491979 chr12 11727969 HOXD11 3237 0.09 trans

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
死神:胎儿(13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene Pearson's Correlation Spearman's Correlation
C3orf39 0.84 0.84
COASY 0.82 0.81
PIGT 0.81 0.84
GRINA 0.81 0.79
FAM73B 0.81 0.80
AP2A1 0.81 0.78
RABGGTA 0.80 0.77
ATG4D 0.80 0.82
SLC27A4 0.80 0.77
ATP13A2 0.80 0.75
Top 10 negatively co-expressed genes
Gene Pearson's Correlation Spearman's Correlation
AF347015.21 -0.56 -0.44
AF347015.18 -0.50 -0.39
AF347015.8 -0.47 -0.37
AL139819.3 -0.47 -0.44
MT-CO2 -0.46 -0.37
AC010300.1 -0.46 -0.47
MT-ATP8 -0.46 -0.39
FAM159B -0.46 -0.59
AF347015.31 -0.46 -0.36
AF347015.2 -0.45 -0.31

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
MYLLYKANGAS AMPLIFICATION HOT SPOT 25 15 6 All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS 1038 678 All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS 1062 725 All SZGR 2.0 genes in this pathway
SHIN B CELL LYMPHOMA CLUSTER 1 13 11 All SZGR 2.0 genes in this pathway
KONDO PROSTATE CANCER HCP WITH H3K27ME3 97 72 All SZGR 2.0 genes in this pathway
GRESHOCK CANCER COPY NUMBER UP 323 240 All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K27ME3 269 159 All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 AND H3K27ME3 349 234 All SZGR 2.0 genes in this pathway
MIKKELSEN MCV6 HCP WITH H3K27ME3 435 318 All SZGR 2.0 genes in this pathway
FONTAINE PAPILLARY THYROID CARCINOMA DN 80 53 All SZGR 2.0 genes in this pathway
MIKKELSEN NPC HCP WITH H3K27ME3 341 243 All SZGR 2.0 genes in this pathway
VANDESLUIS COMMD1 TARGETS GROUP 4 DN 16 11 All SZGR 2.0 genes in this pathway
KOINUMA TARGETS OF SMAD2 OR SMAD3 824 528 All SZGR 2.0 genes in this pathway
KATSANOU ELAVL1 TARGETS DN 148 88 All SZGR 2.0 genes in this pathway